gatk-3.8

Author	SHA1	Message	Date
Mark DePristo	6592972f82	Putative fix for BAQ array out of bounds -- Old code required qual to be <64, which isn't strictly necessary. Now uses the Picard SAMUtils.MAX_PHRED_SCORE constant -- Unittest to enforce this behavior	2011-09-21 11:25:08 -04:00
David Roazen	9d2cda3d41	Removed a public -> private dependency in our test suite.	2011-08-12 17:29:10 -04:00
Mark A. DePristo	defa3cfe85	Moved around private walkers into appropriate directories in private gatk.walkers. Moved a few public walkers into private qc package, and some private qc walkers into the public directory. Removed several obviously broken and/or unused walkers.	2011-06-30 14:59:58 -04:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00